chr2-55235558-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002954.6(RPS27A):āc.452A>Gā(p.Asn151Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000561 in 1,603,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002954.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS27A | NM_002954.6 | c.452A>G | p.Asn151Ser | missense_variant | 6/6 | ENST00000272317.11 | |
RPS27A | NM_001135592.2 | c.452A>G | p.Asn151Ser | missense_variant | 6/6 | ||
RPS27A | NM_001177413.1 | c.452A>G | p.Asn151Ser | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS27A | ENST00000272317.11 | c.452A>G | p.Asn151Ser | missense_variant | 6/6 | 1 | NM_002954.6 | P1 | |
ENST00000686015.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000551 AC: 8AN: 1451506Hom.: 0 Cov.: 31 AF XY: 0.00000692 AC XY: 5AN XY: 722316
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | The c.452A>G (p.N151S) alteration is located in exon 6 (coding exon 5) of the RPS27A gene. This alteration results from a A to G substitution at nucleotide position 452, causing the asparagine (N) at amino acid position 151 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at